• A San Diego firefighter who supplemented $66,539 base pay with $159,017 of overtime for a total of $225,556.

Most of the large payouts on the list were due to employees who accrued and banked vacation and sick days — then took those days in cash at retirement. Cities across the state, such as San Marcos, are phasing out the ability for employees to pile up so much time.

Schaffer, for example was grandfathered in to city rules that allowed such banking.

“Mr. Schafer was a legacy employee,” San Marcos Deputy City Manager Lydia Romero said. “We can’t go back and change the rules, but what we’ve done since 2007 is cap the accrual period of vacation. Workers can only accrue to a certain cap and each of the labor groups have a different cap.”

Schaffer had been with the city more than 30 years, Romero said.

Excluding those who left employment and received a payout in 2012, the highest paid city employee was Escondido City Manager Clay Phillips, who received $277,905, which included $34,607 in travel and car allowance and $22,793 in a payment he received in lieu of taking some vacation time.

Phillips said that taxpayers get their money’s worth. Escondido is a full service city, he noted, and he oversees police, fire and sewer along with a slew of city services.

“It’s just how the market has played out,” Phillips said.

He also said the U-T would likely be calling him about his salary next year, too, given his years of service with the city.

“The numbers are only going to go up,” he said. “That’s a fact.”

Mike Zucchet, general manager of the San Diego Municipal Employees Association, said that it was largely the top brass who got the best paydays.

“Publicizing the high ends of these lists is perhaps more interesting than focusing on the thousands of rank and file workers,” he said. “But the eye-popping compensation packages of some nonunion management employees are simply not representative of the typical city worker.”

One exception was the San Diego frontline firefighter with the large overtime allotment.

Chief Javier Mainar said the firefighter worked a lot of extra shifts at the airport fire station, where there is relatively low activity. The job there is to respond to calls related to plane crashes or other needs on the airfield itself, not in the surrounding neighborhood.

Mainar said the majority of firefighters choose to work overtime, with reasons ranging from bettering their family position to paying for college.

The overtime setup, where firefighters earn 1.5 times their base pay, still makes financial sense for the city, Mainar said, and beats hiring on extra people.

“It is less costly overall to pay existing firefighters to cover these shifts via overtime than it is to hire more firefighters to cover them,” he said.

The city of San Diego paid out more than $62.3 million in overtime pay in 2012, according to the report, or about 9.4 percent of total wages paid. More than half of the overtime payments, or $33.6 million, went to employees of the San Diego Fire-Rescue Department. Eleven fire employees earned six figures in overtime.

The firefighter overtime tab did not surprise San Diego County Taxpayers Association President Felipe Monroig.

“That’s an all too common practice,” Monroig said. “It’s been going on for years with them. They’ll claim that it’s cheaper to pay overtime than it is to hire somebody else, because of the high cost of bringing people into the city. You’re going to see over and over again that their overtime pay is really high.”

Indeed, the city’s overtime payments topped those of San Diego County government, even though the county has a larger total payroll — about 7,000 more employees.

In all, the county paid out nearly $43 million in overtime pay in 2012, or about 4.3 percent of total wages paid. Almost all of the top overtime earners were sheriff’s deputies, plus a couple psychiatrists working for Health and Human Services, and a district attorney’s investigator.

Overtime pay increased 21 percent between 2011 and 2012 for San Diego city employees, even as regular pay decreased 5 percent for city workers, the data showed.

The taxpayers association’s Monroig said it’s important that the controller release this salary data annually.

“For a watchdog organization like ours, having information like this allows us to ask questions,” he said. “And if there is something that we see that we think is outside the scope of reasonable then we advocate for policy changes.”